The Miocene Pebas Formation from the section Santa Rosa de Pichana (Loreto, Peru) was investigated using a combination of analyses of sedimentary facies, molluscan communities and taphonomy, and stable isotopes of both entire shells and growth bands in bivalves. Three sequences, comprising a succession of transgressive, maximum flooding and regressive/prograding intervals, are documented. Molluscs are most common in the transgressive/highstand intervals and are almost absent in regressive/prograding intervals. The fauna is dominated by endemic Pebasian species, such as Pachydon and Dyris spp. The nature of the deposits as well as the availability of oxygen varied in a predictable way within each of the sequences and determined the nature of the assemblages. Highest diversity was reached in the late transgressive phase before the development of dysoxia that was widespread during the late highstand and early regressive/prograding phase. The mollusc and isotope data show no indications of elevated salinities, in contrast to ichnofossils found in the section. This discrepancy is interpreted to result either from temporal separation of the ichnofossils and the mollusc fossils or from evolution beyond usual ecological tolerances of taxa that produced these ichnofossils into freshwater settings.